Variation in microbial and plant associations across wild bee families, functional groups, and urban environments

Abstract Bees harbour diverse microbiomes and floral associations, which may shift in response to several biological and environmental factors. We examined the diversity of bacterial, fungal, and plant associates (i.e. from foraging or nesting material) across 32 bee species from five families (Apidae, Megachilidae, Halictidae, Colletidae, and Andrenidae) using 16S rRNA, ITS1, and rbcL amplicon sequencing. The included bee species represent multiple axes of variation across functional traits including body size, nesting behaviour, sociality, diet, and native status, and response to urbanization. Apidae, Colletidae, and Andrenidae bee families had richer communities of bacterial and plant associates than Halictidae and Megachilidae, while fungal diversity and composition were similar across families. Common microbes and plant associations were detected across the bee community, but certain taxa were common only to specific bee species. Plant associations more often shifted significantly in diversity depending on functional trait and urban intensity, whereas bacterial and fungal diversity were largely consistent across bee families, functional traits, and urban intensities. Our findings show that while microbial communities are fairly stable across bee lineages and functional groups, bee-associated plant communities vary with urbanization and are the primary factor differentiating bee species in urban landscapes.